The "Three Initiates" who authored The Kybalion chose to remain anonymous. As a result, a great deal of speculation has been made about who actually wrote the book.

The most common proposal is that The Kybalion was authored by William Walker Atkinson, either alone or with others. Atkinson was known to use many pseudonyms, and to self-publish his works. He was also the owner of the "Yogi Publication Society of Chicago", the publisher of The Kybalion.

Also suggestive is the fact that, among his earliest published pseudonymous and anonymous works may have been a series entitled The Arcane Teachings, which bears many superficial similarities to The Kybalion -- The Kybalion explores seven "Hermetic Principles" while The Arcane Teachings examines seven "Arcane Laws", The Kybalion claims to be an elucidation of an ancient, unpublished Hermetic text of the same name, while The Arcane Teachings claims to reveal the wisdom of an ancient, unpublished scroll of occult aphorisms, and both books describe three "Great Planes" of reality which are further subdivided into seven lesser planes. Both books also describe three of the lesser planes as "astral black keys" analogous to the black keys on a piano, and inhabited by elemental spirits. And, both books describe the process of "Mental Alchemy" in great detail, and in nearly complete agreement with each other. There are other similarities, and The Arcane Teachings might have been Atkinson's "first draft" of material which later became The Kybalion.

A common theory is that Atkinson co-wrote the book with Paul Foster Case and Michael Whitty. This theory is often held by members of Builders of the Adytum, the Mystery School later founded by Case, though the group doesn't publicly make this claim itself. In fact, this story appears to have originated with a B.O.T.A. splinter group, the Fraternity of Hidden Light.[21]

Along these lines, much has been made about the fact that Paul Foster Case was a Freemason, and that The Kybalion's publisher, the Yogi Publication Society, gave its address as "Masonic Temple, Chicago IL" in the book's frontispiece. However, Chicago's "Masonic Temple" was also the city's first skyscraper, housing dozens of stores and small businesses without any Masonic affiliations, and named for the Masonic Lodge which financed much of its construction and met in its top few floors.[22]

Other names speculatively mentioned as co-authors of The Kybalion include Harriet Case (Paul Foster Case's wife at the time), Ann Davies (who succeeded Paul Foster Case as head of the B.O.T.A.), Mabel Collins (a prominent Theosophical writer), Claude Bragdon (an architect, Theosophist, and writer on "mystic geometry"), and Claude Alexander (a well-known stage magician, mentalist, proponent of crystal gazing, and New Thought author). However, given Atkinson's prolific output under almost a dozen pseudonyms, it is debatable whether he would have needed or sought a co-author for the book.